Genome Landscapes and Bacteriophage Codon Usage

Figure 5

Observed and randomized landscapes for lambda phage.

Observed landscapes are shown along with randomized landscapes associated with the green and orange tests. The green randomization procedure tests the significance of the GC3 landscape controlling for the observed CAI (actually, BCAI) variation across the genome. The orange randomization procedure tests the significance of the BCAI landscape, controlling for the observed GC3 variation across the genome. Both tests preserve the amino-acid sequence exactly. Both observed landscapes lie outside the distribution of random trials, indicating there is non-random GC3 content controlling for CAI, and non-random CAI content controlling for GC3.